Integrated Bioinformatics Analysis Revealing that the NSDHL Gene Might Be Associated with the Progression of Western HFD/SW-Induced Hepatocellular Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40033501", "kind": "science-record", "revision": 3, "content_hash": "sha256:a658f65ec21bf0ccc975b4428601854c3efc78bb87bc8fd4342aa5dfa55e87ff", "created_at": "2026-11-01T20:30:15Z", "updated_at": "2026-11-01T22:13:42Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Bioinformatics Analysis Revealing that the NSDHL Gene Might Be Associated with the Progression of Western HFD/SW-Induced Hepatocellular Carcinoma.", "doi": "10.2174/0118715303356256250129063049", "pmid": "40033501", "authors": ["Jing Hong", "Bo Pan", "Zhaoxian Yan", "Xiao-Feng Zhai", "Yongshang Liu"], "journal": "Endocrine, metabolic & immune disorders drug targets", "year": 2025, "abstract": "BACKGROUND AND OBJECTIVE: Hepatocellular carcinoma (HCC) remains a significant global health concern. However, the etiology and pathogenesis of HCC have yet to be fully elucidated. Previous studies have indicated a close association between obesity and the occurrence and progression of HCC. The objective of this study was to employ bioinformatics strategies in order to explore key genes associated with the clinical diagnosis and prognosis of HCC induced by a Western high-fat diet and sugar water (HFD/SW).\nMATERIALS AND METHODS: We obtained the expression profile chip data GSE197884 from the Gene Expression Omnibus (GEO) database. Subsequently, \"DESeq\" and \"Limma\" R packages were employed to identify differentially expressed genes (DEGs) while constructing a co-expressed gene network using weighted gene co-expression analysis (WGCNA). Functional enrichment analyses were then carried out, followed by the construction of a protein-protein interaction (PPI) network to uncover core genes. The core genes were confirmed through data retrieved from The Cancer Genome Atlas (TCGA) database in order to determine their status as hub genes. Finally, survival and tumor immune infiltration analyses were performed to unveil the prognostic significance of these hub genes.\nRESULTS: In total, 126 intersection targets were retrieved through the Venn diagram. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that the DEGs were primarily related to the proliferation and apoptosis of HCC cells, the digestion and metabolism of liver cells, the HCC tumor microenvironment, and immune response. The PPI network analysis identified 11 core targets, among which seven hub genes, including NSDHL, MVK, SQLW, GCAT, ALAS2, GLDC, and AGXT, were obtained after TCGA database validation. Furthermore, it was found that NSDHL was closely associated with the clinical diagnosis and prognosis of HCC induced by HFD/SW and also affected the cellular immune infiltration in the HCC tumor microenvironment.\nCONCLUSION: The present study demonstrated a significantly elevated expression of NSDHL in HCC tissues, suggesting its potential as a specific biomarker for precise clinical diagnosis and prognosis assessment of HCC induced by HFD/SW.", "claims": [{"id": "claim-method", "statement": "WGCNA was applied to identify modules of highly correlated genes among samples and establish associations with external sample traits.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40033501", "locator": "sections[4] \"WGCNA-Based Identification of Key Gene Co-Expression Modules, Differential Expression Analysis, and Intersection with WGCNA Differential Modules\" paragraph 2", "quote": "WGCNA was applied to identify modules of highly correlated genes among samples and establish associations with external sample traits."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data and supportive information are available within the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40033501", "locator": "sections[25] \"AVAILABILITY OF DATA AND MATERIALS\" paragraph 2", "quote": "The data and supportive information are available within the article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The present study demonstrated a significantly elevated expression of NSDHL in HCC tissues, suggesting its potential as a specific biomarker for precise clinical diagnosis and prognosis assessment of HCC induced by HFD/SW.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40033501", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "The present study demonstrated a significantly elevated expression of NSDHL in HCC tissues, suggesting its potential as a specific biomarker for precise clinical diagnosis and prognosis assessment of HCC induced by HFD/SW."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The present study demonstrated a significantly elevated expression of NSDHL in HCC tissues, suggesting its potential as a specific biomarker for precise clinical diagnosis and prognosis assessment of HCC induced by HFD/SW.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:40033501"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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